Contamination of food by harmful microorganisms causes deterioration in quality of the food. For example, contamination of malt alcoholic beverages by harmful microorganisms causes turbidity and/or degradation of flavor of the beverages. Moreover, contamination of beer by Brettanomyces (Dekkera), Candida, Pichia, Hanseniaspora, Saccharomyces with exception of those for brewery yeasts, and the like, deteriorates the quality of the beer, causing turbidity and/or off-flavor. Currently, the most commonly used method for detecting the harmful microorganisms in beer is a method that comprises filtering beer of interest through a membrane filter, thereafter culturing the beer and detecting a colony that has grown.
Further, in order to determine whether the colony is the one that corresponds to the harmful microorganisms, a method that comprises performing PCR with a primer specific to the harmful organisms using a DNA extracted from the colony as a template, and determining whether a PCR product is obtained by electrophoresis is used (see, for example, Japanese Laid-open Patent Publication No. 7-289295). However, this method is extremely cumbersome and time consuming because a multiple runs of PCR must be performed for each microorganism using a large numbers of primers. A large numbers of primers may be used as a mixture in a single tube for amplification reactions in order to shorten the time required for the method. However, the number of available primers is limited and it is difficult to perform precise determination provided there is trace amount of specimen.
In order to solve these problems, there have been proposed different methods of identifying microorganisms. In these methods, primers are designed in such a manner that only a portion of a gene that commonly exists across different microorganisms and that contains species-specific sequences is amplified. After the amplification, the amplified product is excised by restriction enzymes that recognize the species-specific sequences, and microorganisms are identified based on the band size obtained by electrophoresis. However, it is not necessarily the case that such restriction enzymes are available for all species of microorganisms to be tested. Further, since the methods require the highly complicated procedure of excising the amplified product with several different kinds of restriction enzymes for electrophoresis, the methods are also problematic in terms of speed and readiness.
Further, a method, in which a species-specific sequence is used as a probe, and the presence or absence of a complementary sequence in the tested DNA or RNA is determined by hybridization, has been used to solve these problems.